I have just updated to 12.04 and I am trying to assign two finger tap to my track pad. I know the code, just need to understand how to set it permanently because at the moment I need to input the code into the terminal every time I log on.

You can create a script and add it to your startup applications

Make it executable by opening a terminal and typing/running the following command:

chmod +x ~/Documents/mouseMod

Finally, add the file to your startup applications (I'm not sure where it is in 12.04, but in 11.10 I found it by searching for startup in the dash) by clicking add and browsing to/selecting the script (i.e. mouseMod).